| Name | Namespace | Definition |
| NARCIS |
narcis |
NARCIS provides access to scientific information, including (open access) publications from the repositories of all the Dutch universities, KNAW, NWO and a number of research institutes, which is not referenced in other citation databases. |
| 3DMET |
3dmet |
3DMET is a database collecting three-dimensional structures of natural metabolites. |
| KEGG Pathway |
kegg.pathway |
KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks. |
| KEGG Metagenome |
kegg.metagenome |
The KEGG Metagenome Database collection information on environmental samples (ecosystems) of genome sequences for multiple species. |
| KEGG Genome |
kegg.genome |
KEGG Genome is a collection of organisms whose genomes have been completely sequenced. |
 CAS |
cas |
CAS (Chemical Abstracts Service) is a division of the American Chemical Society and is the producer of comprehensive databases of chemical information. |
| nextProt |
nextprot |
neXtProt is a resource on human proteins, and includes information such as proteins’ function, subcellular location, expression, interactions and role in diseases. |
| WormBase |
wormbase |
WormBase is an online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans and related nematodes. It is used by the C. elegans research community both as an information resource and as a mode to publish and distribute their results. |
| EDAM Ontology |
edam |
EDAM is an ontology of general bioinformatics concepts, including topics, data types, formats, identifiers and operations. EDAM provides a controlled vocabulary for the description, in semantic terms, of things such as: web services (e.g. WSDL files), applications, tool collections and packages, work-benches and workflow software, databases and ontologies, XSD data schema and data objects, data syntax and file formats, web portals and pages, resource catalogues and documents (such as scientific publications). |
| LIPID MAPS |
lipidmaps |
The LIPID MAPS Lipid Classification System is comprised of eight lipid categories, each with its own subclassification hierarchy. All lipids in the LIPID MAPS Structure Database (LMSD) have been classified using this system and have been assigned LIPID MAPS ID's which reflects their position in the classification hierarchy. |
| Entrez Gene |
entrez.gene |
Entrez Gene is the NCBI's database for gene-specific information, focusing on completely sequenced genomes, those with an active research community to contribute gene-specific information, or those that are scheduled for intense sequence analysis. |
| CATH superfamily |
cath.superfamily |
The CATH database is a hierarchical domain classification of protein structures in the Protein Data Bank. Protein structures are classified using a combination of automated and manual procedures. There are four major levels in this hierarchy; Class (secondary structure classification, e.g. mostly alpha), Architecture (classification based on overall shape), Topology (fold family) and Homologous superfamily (protein domains which are thought to share a common ancestor). This colelction is concerned with superfamily classification. |
| Taxonomy |
taxonomy |
The taxonomy contains the relationships between all living forms for which nucleic acid or protein sequence have been determined. |
| Ontology of Physics for Biology |
opb |
The OPB is a reference ontology of classical physics as applied to the dynamics of biological systems. It is designed to encompass the multiple structural scales (multiscale atoms to organisms) and multiple physical domains (multidomain fluid dynamics, chemical kinetics, particle diffusion, etc.) that are encountered in the study and analysis of biological organisms. |
| Cell Cycle Ontology |
cco |
The Cell Cycle Ontology is an application ontology that captures and integrates detailed knowledge on the cell cycle process. |
| Human Disease Ontology |
obo.do |
The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing the biomedical community with consistent, reusable and sustainable descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. |
| eggNOG |
eggnog |
eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the genes based on their various annotations), with functional categories (i.e derived from the original COG/KOG categories). |
| Gramene genes |
gramene.gene |
Gramene is a comparative genome mapping database for grasses and crop plants. It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, quantitative trait loci (QTL), and publications, with a curated database of mutants (genes and alleles), molecular markers, and proteins. This datatype refers to genes in Gramene. |
| iRefWeb |
irefweb |
iRefWeb is an interface to a relational database containing the latest build of the interaction Reference Index (iRefIndex) which integrates protein interaction data from ten different interaction databases: BioGRID, BIND, CORUM, DIP, HPRD, INTACT, MINT, MPPI, MPACT and OPHID. In addition, iRefWeb associates interactions with the PubMed record from which they are derived. |
| miRBase mature sequence |
mirbase.mature |
The miRBase Sequence Database is a searchable database of published miRNA sequences and annotation. This collection refers specifically to the mature miRNA sequence. |
| Cell Type Ontology |
obo.clo |
The Cell Ontology is designed as a structured controlled vocabulary for cell types. The ontology was constructed for use by the model organism and other bioinformatics databases, incorporating cell types from prokaryotes to mammals, and includes plants and fungi. |
| Chemical Component Dictionary |
pdb-ccd |
The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in Protein Data Bank entries. It contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, aromatic bond assignments, idealized coordinates, chemical descriptors (SMILES & InChI), and systematic chemical names. |
| BioModels Database |
biomodels.db |
BioModels Database is a data resource that allows biologists to store, search and retrieve published mathematical models of biological interests. |
| Saccharomyces genome database pathways |
sgd.pathways |
Curated biochemical pathways for Saccharomyces cerevisiae at Saccharomyces genome database (SGD). |
| VectorBase |
vectorbase |
VectorBase is an NIAID-funded Bioinformatic Resource Center focused on invertebrate vectors of human pathogens. VectorBase annotates and curates vector genomes providing a web accessible integrated resource for the research community. Currently, VectorBase contains genome information for three mosquito species: Aedes aegypti, Anopheles gambiae and Culex quinquefasciatus, a body louse Pediculus humanus and a tick species Ixodes scapularis. |
| SWISS-MODEL |
swiss-model |
The SWISS-MODEL Repository is a database of 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for sequences registered is SWISS-PROT. |
| REBASE |
rebase |
REBASE is a comprehensive database of information about restriction enzymes, DNA methyltransferases and related proteins involved in the biological process of restriction-modification (R-M). It contains fully referenced information about recognition and cleavage sites, isoschizomers, neoschizomers, commercial availability, methylation sensitivity, crystal and sequence data. |
| ProtoNet Cluster |
protonet.cluster |
ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references cluster information. |
| ProtoNet ProteinCard |
protonet.proteincard |
ProtoNet provides automatic hierarchical classification of protein sequences in the UniProt database, partitioning the protein space into clusters of similar proteins. This collection references protein information. |
| CutDB |
pmap.cutdb |
The Proteolysis MAP is a resource for proteolytic networks and pathways. PMAP is comprised of five databases, linked together in one environment. CutDB is a database of individual proteolytic events (cleavage sites). |
